What happens if 2 genes have the same connection but a different innovation number?
When do mutations occur and between which nodes?


There are two types of mutations in the NEAT model, each of them appears randomly during one epoch on different individuals; the number of structures affected by mutations may vary depending upon the nature of the problem.


A new gene/node is added to the structure and properly linked.
A new connection between two nodes is added.



  When mating, what happens if 2 genes have the same connection but a different innovation number?


During a single epoch/generation every mutation is tracked and if the same mutation appears it can't have the same global innovation number. Same mutation, same innovation number. In that way, during the mating phase, there is no decisional problem which leads to prefer one structure to the other.